Diffusional correlations among multiple active sites in a single enzyme
Diffusional correlations among multiple active sites in a single enzyme
Publication Type:
Journal ArticleSource:
Physical Chemistry Chemical Physics, Volume 16, Number 13, p.6211-6216 (2014)URL:
https://www.scopus.com/inward/record.uri?eid=2-s2.0-84896755155&doi=10.1039%2fc3cp55252g&partnerID=40&md5=8ddc5f17dc288a66862f94bba6391775Keywords:
4-oxalocrotonate tautomerase, binding site, Binding Sites, Catalytic Domain, chemistry, Diffusion, enzyme, enzyme active site, enzyme specificity, Enzymes, isomerase, Isomerases, Kinetics, metabolism, Molecular dynamics, Molecular Dynamics Simulation, Protein Binding, Substrate SpecificityAbstract:
Simulations of the enzymatic dynamics of a model enzyme containing multiple substrate binding sites indicate the existence of diffusional correlations in the chemical reactivity of the active sites. A coarse-grain, particle-based, mesoscopic description of the system, comprising the enzyme, the substrate, the product and solvent, is constructed to study these effects. The reactive and non-reactive dynamics is followed using a hybrid scheme that combines molecular dynamics for the enzyme, substrate and product molecules with multiparticle collision dynamics for the solvent. It is found that the reactivity of an individual active site in the multiple-active-site enzyme is reduced substantially, and this effect is analyzed and attributed to diffusive competition for the substrate among the different active sites in the enzyme. This journal is © 2014 the Owner Societies.
